September 2008 E-Phys Protocol

Microelectrode array experiments
If the new electrodes are ready, it will be a top priority to investigate their properties.
Some things to look at: Recording

1. Stimulus selectivity

How does the stimulus-selectivity of microelectrodes differ from large electrodes?

How does stimulus-selectivity vary within a single microelectrode array (MEA)?

2. Response latency/duration

Within an object-selective visual area, do different patches of cortex depolarize at different latencies or for different durations?

3. Receptive Field Size

Do small electrodes have different RFs than big electrodes?

How does RF size vary within and between object-selective visual areas?

4. Gamma oscillation

Are oscillations in the gamma band more correlated among nearby electrodes than far electrodes?

5. Adaptation

Do microelectrodes demonstrate different adaptation behavior than large electrodes?

Do different microelectrodes within an ME array adapt differently to the same repeated stimuli?

6. Choice probability

Does the pattern of activity in object-selective cortical areas (as measured by MEAs) correlate in any way with the subject's behavior?

Stimulation

1. Perception thresholds

Perception thresholds may be lower with microelectrodes because of high current density.

2. Percepts in higher visual areas

If the microelectrodes have smaller RFs or are more feature-selective than the large electrodes, it could mean that sending current through them would activate a more functionally-segregated group of neurons than has previously been possible. If so, microstimulation with microelectrodes may be more likely to evoke percepts in higher-level visual areas than with the large electrodes.

• trial structure: 8 nonselective stimuli, 8 of the same selective stimulus, 8 nonselective stimuli, 8 different selective stimuli. Stopsign appear at random or at the end of each run.

• A rudimentary way to approximate this would be to have several copies of the same image in the image folder, and selecting all of them in the selectivity plugin.

Notes:

• Now that we can record from all the electrodes simultaneously, it will be less important to identify selective categories. By showing equal amount of all the categories, we can get good sample sizes for several differently-selective electrodes.

•It would be nice to have a modified version of the current Selectivity plugin to satisfy these conditions:

1. the patient is supposed to press the button after stop-signs instead of after repeats

2. Selective stimuli are directly repeated every 8-12 images

3. The stimulus preceding the repeat is always a nonselective stimulus

Processing Subject Data

After obtaining the CD containing the patient CT data from St. Luke's, use OsiriX to export all images
(using the export to DICOM option, and the hierarchical, uncompress options).

CT scans have voxel size 0.488x0.488x1 mm; this may need to be adjusted manually with

3drefit -zdel 1.000 DE_CTSDE+orig

(If the CTs look distorted in AFNI, then the voxel size must be adjusted).
Next, the CTs must be registered with the hi-res presurgical MRI anatomy.
This may fail because the CT has a coordinate system with a very different origin than the MRI.
Registration routines will not work if the input datasets are not in rough alignment.
To check this, type

Check in AFNI to make sure that they alignment is correct. NB: It is also possible to crop the MRI before Allineating since the MR coverage is typically greater than the CT coverage. In a test case, this did not have a big effect.

Next, the electrodes positions are manually located and saved as Tags. Then, these positions can be used to create an Electrodes file for display as spheres in SUMA.
To label the electrodes, a separate .niml.do file can be created with the label for each electrode.

Things to do

Can stimuli be vector-based rather than pixel based, so as not to lose resolution with scaling? POSSIBLE if original file is vector-based

Enable online scrambling LOOKING INTO IT

Enable online color to black and white conversion LOOKING INTO IT

HumanLetterDetection

Analyze data from LR to see where the RFs are

DEBUGGING KNOT PROBLEMS

First, quit Knot.
Then, unplug one ITC from the USB port, wait for the power light to go off, plug it back in.
Repeat this, one at a time, for all ITCs.
Before beginning experiment, always make sure you get nice traces in Channel Data window, not just flat lines (even if looks nice on oscilloscope).